import java.io.File;
import java.io.IOException;
-import java.io.Writer;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.sdi.GSDI;
import org.forester.sdi.SDI;
import org.forester.sdi.SDI.TaxonomyComparisonBase;
import org.forester.sdi.SDIse;
+import org.forester.sdi.SdiException;
import org.forester.util.CommandLineArguments;
+import org.forester.util.EasyWriter;
+import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
public final class gsdi {
GSDI, SDI
}
final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
- final static private String STRIP_OPTION = "s";
final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g";
final static private String SDI_OPTION = "b";
final static private String MOST_PARSIMONIOUS_OPTION = "m";
final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q";
final static private String HELP_OPTION_1 = "help";
final static private String HELP_OPTION_2 = "h";
- final static private String DEFAULT_OUTFILE_SUFFIX = "_gsdi_out.phylo.xml";
+ final static private String DEFAULT_OUTFILE_SUFFIX = "_gsdi_out.xml";
final static private String SUFFIX_FOR_LIST_OF_STIPPED_GENE_TREE_NODES = "_stripped_gene_tree_nodes.txt";
+ final static private String SUFFIX_FOR_SPECIES_TREE_USED = "_species_tree_used.xml";
final static private String LOGFILE_SUFFIX = "_gsdi_log.txt";
final static private String PRG_NAME = "gsdi";
final static private String PRG_VERSION = "0.901";
System.exit( -1 );
}
final List<String> allowed_options = new ArrayList<String>();
- allowed_options.add( gsdi.STRIP_OPTION );
allowed_options.add( gsdi.SDI_OPTION );
allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
private static void execute( final CommandLineArguments cla ) throws IOException {
BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI;
- boolean strip = false;
boolean most_parsimonous_duplication_model = false;
boolean species_tree_in_phyloxml = true;
boolean allow_stripping_of_gene_tree = false;
- if ( cla.isOptionSet( gsdi.STRIP_OPTION ) ) {
- strip = true;
- }
if ( cla.isOptionSet( gsdi.SDI_OPTION ) ) {
base_algorithm = BASE_ALGORITHM.SDI;
}
File species_tree_file = null;
File out_file = null;
File log_file = null;
- Writer log_writer = null;
+ EasyWriter log_writer = null;
try {
gene_tree_file = cla.getFile( 0 );
species_tree_file = cla.getFile( 1 );
ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
}
try {
- log_writer = ForesterUtil.createBufferedWriter( log_file );
+ log_writer = ForesterUtil.createEasyWriter( log_file );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
final TaxonomyComparisonBase comp_base = GSDI.determineTaxonomyComparisonBase( gene_tree );
switch ( comp_base ) {
case SCIENTIFIC_NAME:
- PhylogenyMethods
- .transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID_UNIPROT_1 );
+ try {
+ PhylogenyMethods
+ .transferNodeNameToField( species_tree,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+ true );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME,
+ "Failed to transfer general node name to scientific name, in ["
+ + species_tree_file + "]: " + e.getMessage() );
+ }
break;
case CODE:
- PhylogenyMethods.transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE );
+ try {
+ PhylogenyMethods
+ .transferNodeNameToField( species_tree,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
+ true );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME,
+ "Failed to transfer general node name to taxonomy code, in ["
+ + species_tree_file + "]: " + e.getMessage() );
+ }
break;
case ID:
- PhylogenyMethods.transferNodeNameToField( species_tree,
- PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID );
+ try {
+ PhylogenyMethods.transferNodeNameToField( species_tree,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
+ true );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ ForesterUtil.fatalError( gsdi.PRG_NAME,
+ "Failed to transfer general node name to taxonomy id, in ["
+ + species_tree_file + "]: " + e.getMessage() );
+ }
break;
default:
ForesterUtil.fatalError( gsdi.PRG_NAME, "unable to determine comparison base" );
}
}
catch ( final IOException e ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME,
- "Failed to read species tree from [" + gene_tree_file + "]: " + e.getMessage() );
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to read species tree from [" + species_tree_file + "]: "
+ + e.getMessage() );
}
gene_tree.setRooted( true );
species_tree.setRooted( true );
if ( !gene_tree.isCompletelyBinary() ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree (\"" + gene_tree_file + "\") is not completely binary" );
+ log_writer.println( "User Error: gene tree is not completely binary" );
+ log_writer.close();
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree is not completely binary" );
}
if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
if ( !species_tree.isCompletelyBinary() ) {
- ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree (\"" + species_tree_file
- + "\") is not completely binary, use GSDI instead" );
+ log_writer.println( "User Error: species tree is not completely binary, use GSDI instead" );
+ log_writer.close();
+ ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree is not completely binary, use GSDI instead" );
}
}
// For timing.
// Helper.randomizeSpecies( 1, 8192, gene_tree );
// Helper.intervalNumberSpecies( gene_tree, 4096 );
// Helper.numberSpeciesInDescOrder( gene_tree );
- log_writer.write( PRG_NAME + " " + PRG_VERSION + " " + PRG_DATE );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
- log_writer.write( PRG_DESC );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
- log_writer.write( PRG_DESC );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
- log_writer.write( new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.println( PRG_NAME + " - " + PRG_DESC );
+ log_writer.println( " version : " + PRG_VERSION );
+ log_writer.println( " date : " + PRG_DATE );
+ log_writer.println( " forester version: " + ForesterConstants.FORESTER_VERSION );
+ log_writer.println( "Start time: " + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
+ log_writer.println( "Gene tree file: " + gene_tree_file.getCanonicalPath() );
+ log_writer.println( "Gene tree name: "
+ + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
+ log_writer.println( "Species tree file: " + species_tree_file.getCanonicalPath() );
+ log_writer.println( "Species tree name: "
+ + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
System.out.println();
- System.out.println( "Strip species tree: " + strip );
- log_writer.write( "Strip species tree: " + strip );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
SDI sdi = null;
final long start_time = new Date().getTime();
try {
System.out.println();
System.out.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
System.out.println( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
- log_writer.write( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
log_writer.write( "Allow stripping of gene tree nodes : " + allow_stripping_of_gene_tree );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.flush();
sdi = new GSDI( gene_tree,
species_tree,
most_parsimonous_duplication_model,
- allow_stripping_of_gene_tree );
+ allow_stripping_of_gene_tree,
+ true );
}
else {
System.out.println();
System.out.println( "Using SDIse algorithm" );
- log_writer.write( "Using SDIse algorithm" );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.println( "Using SDIse algorithm" );
+ log_writer.flush();
sdi = new SDIse( gene_tree, species_tree );
}
}
- catch ( final Exception e ) {
+ catch ( final SdiException e ) {
+ log_writer.println( "User Error: " + e.getLocalizedMessage() );
+ log_writer.close();
ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
}
+ catch ( final IOException e ) {
+ log_writer.println( "Error: " + e );
+ log_writer.close();
+ ForesterUtil.fatalError( PRG_NAME, e.toString() );
+ }
+ catch ( final Exception e ) {
+ log_writer.println( "Error: " + e );
+ log_writer.close();
+ e.printStackTrace();
+ System.exit( -1 );
+ }
System.out.println();
System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
- log_writer.write( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
try {
final PhylogenyWriter writer = new PhylogenyWriter();
writer.toPhyloXML( out_file, gene_tree, 0 );
ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + out_file + "]: " + e.getMessage() );
}
System.out.println();
- System.out.println( "Successfully wrote resulting gene tree to: " + out_file );
+ System.out.println( "Wrote resulting gene tree to: " + out_file );
System.out.println();
- log_writer.write( "Wrote resulting gene tree to: " + out_file );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.println( "Wrote resulting gene tree to: " + out_file );
if ( base_algorithm == BASE_ALGORITHM.SDI ) {
sdi.computeMappingCostL();
System.out.println( "Mapping cost : " + sdi.computeMappingCostL() );
- log_writer.write( "Mapping cost : " + sdi.computeMappingCostL() );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.println( "Mapping cost : " + sdi.computeMappingCostL() );
}
System.out.println( "Number of duplications : " + sdi.getDuplicationsSum() );
- log_writer.write( "Number of duplications : " + sdi.getDuplicationsSum() );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
- if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) && !most_parsimonous_duplication_model ) {
- final int duplications = ( ( GSDI ) sdi ).getSpeciationOrDuplicationEventsSum();
- System.out.println( "Number of potential duplications: " + duplications );
- log_writer.write( "Number of potential duplications: " + duplications );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
- }
- if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
- final int spec = ( ( GSDI ) sdi ).getSpeciationsSum();
+ log_writer.println( "Number of duplications : " + sdi.getDuplicationsSum() );
+ if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
+ final GSDI gsdi = ( GSDI ) sdi;
+ final File species_tree_used_file = new File( out_file + SUFFIX_FOR_SPECIES_TREE_USED );
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( species_tree_used_file, gsdi.getSpeciesTree(), 0 );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "Failed to write to [" + species_tree_used_file + "]: " + e.getMessage() );
+ }
+ System.out.println();
+ System.out.println( "Wrote used species tree to: " + species_tree_used_file );
+ System.out.println();
+ log_writer.println( "Wrote used species tree to: " + species_tree_used_file );
+ if ( !most_parsimonous_duplication_model ) {
+ final int duplications = gsdi.getSpeciationOrDuplicationEventsSum();
+ System.out.println( "Number of potential duplications: " + duplications );
+ log_writer.println( "Number of potential duplications: " + duplications );
+ }
+ final int spec = gsdi.getSpeciationsSum();
System.out.println( "Number of speciations : " + spec );
- log_writer.write( "Number of speciations : " + spec );
- log_writer.write( ForesterUtil.LINE_SEPARATOR );
+ log_writer.println( "Number of speciations : " + spec );
+ for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
+ System.out.println( n.toString() );
+ }
}
System.out.println();
+ log_writer.close();
// some stat on gene tree:
// filename, name
// number of external nodes, strppided nodes
System.out.println();
System.out.println( "Options:" );
// System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION + ": to allow stripping of gene tree nodes without a matching species in the species tree (writes list of stripped nodes to " + );
- System.out.println( " -" + gsdi.STRIP_OPTION
- + ": to strip the species tree of unneeded species prior to duplication inference" );
System.out.println( " -" + gsdi.SDI_OPTION + ": to use SDI algorithm instead of GSDI algorithm" );//TODO gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION not allowed
System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION
+ ": use most parimonious duplication model for GSDI: " );
git://source.jalview.org / jalview.git / blobdiff